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Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment benzene-1,2,4-tricarboxylic acid from single soak
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.091 α = 90 b = 105.628 β = 90 c = 194.028 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 300 mm CCD 2016-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.78 50 100 0.078 0.034 32.7 6.3 99895
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 100 0.918 0.405 0.769 3.1 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JY1 1.78 37.082 1.34 99608 1996 99.98 0.1801 0.1794 0.1801 0.2145 0.2143
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.482 f_angle_d 0.818 f_chiral_restr 0.057 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7003 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing